# this cell is tagged as parameters for `papermill` parameterization
nipah_config = None
altair_config = None
surface = None

#input files
e2_distances_file = None
func_scores_E2_file = None
func_scores_E3_file = None
concat_df_file = None
merged_df_file = None

#output files
contact_type_plot = None
E2_E3_entry_corr_plot = None
E2_E3_entry_all_muts_plot = None
combined_E2_E3_correlation_plots = None
entry_region_boxplot_plot = None
combined_region_barplot_output = None

# Parameters
func_scores_E2_file = "results/filtered_data/entry/e2_entry_filtered.csv"
func_scores_E3_file = "results/filtered_data/entry/e3_entry_filtered.csv"
e2_distances_file = "results/distances/2vsm_distances.csv"
contact_type_plot = "results/images/contact_type_plot.html"
merged_df_file = "results/filtered_data/entry/e2_e3_entry_filter_merged.csv"
concat_df_file = "results/filtered_data/entry/e2_e3_entry_filter_concat.csv"
E2_E3_entry_corr_plot = "results/images/E2_E3_entry_corr_plot.html"
E2_E3_entry_all_muts_plot = "results/images/E2_E3_entry_all_muts_plot.html"
combined_E2_E3_correlation_plots = (
    "results/images/combined_E2_E3_correlation_plots.html"
)
nipah_config = "nipah_config.yaml"
altair_config = "data/custom_analyses_data/theme.py"
entry_region_boxplot_plot = "results/images/entry_region_boxplot_plot.html"
surface = "data/custom_analyses_data/surface_exposure.csv"
combined_region_barplot_output = "results/images/combined_region_barplot_output.html"

import math
import os
import re
import altair as alt

import numpy as np

import pandas as pd

import scipy.stats

#import Bio.SeqIO

import yaml

#from Bio import AlignIO
#from Bio import PDB
#from Bio.Align import PairwiseAligner

# allow more rows for Altair
_ = alt.data_transformers.disable_max_rows()

if os.getcwd() == '/fh/fast/bloom_j/computational_notebooks/blarsen/2023/Nipah_Malaysia_RBP_DMS/':
    pass
    print("Already in correct directory")
else:
    os.chdir("/fh/fast/bloom_j/computational_notebooks/blarsen/2023/Nipah_Malaysia_RBP_DMS/")
    print("Setup in correct directory")

Setup in correct directory

if nipah_config is None:
    e2_distances_file = "results/distances/2vsm_distances.csv"
    func_scores_E2_file = "results/filtered_data/entry/e2_entry_filtered.csv"
    func_scores_E3_file = "results/filtered_data/entry/e3_entry_filtered.csv"
    
    concat_df_file = "results/filtered_data/entry/e2_e3_entry_filter_concat.csv"
    merged_df_file = "results/filtered_data/entry/e2_e3_entry_filter_merged.csv"
    
    nipah_config = "nipah_config.yaml"
    altair_config = "data/custom_analyses_data/theme.py"
    
    surface = "data/custom_analyses_data/surface_exposure.csv"

if altair_config:
    with open(altair_config, 'r') as file:
        exec(file.read())

with open(nipah_config) as f:
    config = yaml.safe_load(f)

#Import filtered entry scores from different selections
func_scores_E2 = pd.read_csv(func_scores_E2_file)
func_scores_E3 = pd.read_csv(func_scores_E3_file)
concat_df = pd.read_csv(concat_df_file) #concatanated entry scores
merged_df = pd.read_csv(merged_df_file) #merged entry scores

def calculate_stats(df, name):
    print(f"For {name}:")
    total_mut = (532) * 19 #total number of possible amino acids
    print(f'There are {total_mut} amino acid mutations possible')
    muts_present = df["effect"].shape[0]
    fraction_muts = muts_present / total_mut
    print(
        f"fraction muts present in {name} is {fraction_muts:.2f} {muts_present}/{total_mut}"
    )

    # Break mutations into bins (negative, neutral, positive) and calculate how many mutants there are
    deleterious_muts = df[df["effect"] <= -0.5].shape[0] 
    neutral_muts = df[(df["effect"] > -0.5) & (df["effect"] < 0.5)].shape[0]
    positive_muts = df[df["effect"] > 0.5].shape[0]

    frac_bad_muts = deleterious_muts / muts_present
    frac_neutral_muts = neutral_muts / muts_present
    frac_pos_muts = positive_muts / muts_present
    print(
        f"The number of deleterious mutants for {name} is {frac_bad_muts:.2f} {deleterious_muts}/{muts_present}"
    )
    print(
        f"The number of neutral mutants for {name} is {frac_neutral_muts:.2f} {neutral_muts}/{muts_present}"
    )
    print(
        f"The number of positive mutants for {name} is {frac_pos_muts:.2f} {positive_muts}/{muts_present}\n"
    )

calculate_stats(func_scores_E2, "CHO-bEFNB2")
calculate_stats(func_scores_E3, "CHO-bEFNB3")

For CHO-bEFNB2:
There are 10108 amino acid mutations possible
fraction muts present in CHO-bEFNB2 is 0.97 9786/10108
The number of deleterious mutants for CHO-bEFNB2 is 0.44 4296/9786
The number of neutral mutants for CHO-bEFNB2 is 0.54 5303/9786
The number of positive mutants for CHO-bEFNB2 is 0.02 186/9786

For CHO-bEFNB3:
There are 10108 amino acid mutations possible
fraction muts present in CHO-bEFNB3 is 0.96 9713/10108
The number of deleterious mutants for CHO-bEFNB3 is 0.43 4182/9713
The number of neutral mutants for CHO-bEFNB3 is 0.56 5451/9713
The number of positive mutants for CHO-bEFNB3 is 0.01 80/9713

def overall_stats_all_neg(df,effect,name,region=None):
    print(f'We are analyzing data for {name}:')
    
    if region is None:
        contact_df = df
    else:
        contact_df = df[df['site'].isin(region)]
    
    filtered_df = contact_df.groupby('site').filter(lambda group: (group['effect'] < 0).all())
    unique = filtered_df['site'].unique()
    print(list(unique))
    total_sites = contact_df['site'].unique().shape[0]
    subset = filtered_df['site'].unique().shape[0]
       
    fraction = subset/total_sites
    percent = fraction * 100
    print(f'The total number of sites are: {total_sites}\n')
    print(f' The number of sites where all mutants are negative for {effect}: {subset}\n')
    print(f' The percent of sites where all mutants are negative for {effect}: {percent:.0f}\n')
    return unique

intolerant_sites_E2 = list(overall_stats_all_neg(func_scores_E2,'effect','CHO-bEFNB2'))
intolerant_sites_E3 = list(overall_stats_all_neg(func_scores_E3,'effect','CHO-bEFNB3'))

We are analyzing data for CHO-bEFNB2:
[79, 80, 95, 97, 106, 107, 111, 112, 113, 120, 121, 125, 126, 127, 128, 130, 138, 146, 151, 157, 158, 159, 160, 161, 162, 163, 165, 167, 172, 189, 203, 205, 206, 207, 208, 216, 229, 233, 240, 246, 251, 253, 254, 257, 258, 259, 260, 262, 263, 264, 266, 267, 298, 303, 320, 323, 331, 347, 355, 382, 387, 395, 412, 439, 454, 460, 467, 487, 489, 493, 499, 500, 503, 506, 510, 537, 563, 565, 573, 574, 575, 594, 598]
The total number of sites are: 532

 The number of sites where all mutants are negative for effect: 83

 The percent of sites where all mutants are negative for effect: 16

We are analyzing data for CHO-bEFNB3:
[100, 104, 107, 108, 109, 111, 112, 113, 120, 121, 126, 138, 146, 158, 159, 162, 163, 206, 207, 208, 216, 220, 229, 236, 240, 243, 251, 253, 257, 258, 259, 260, 263, 266, 276, 303, 347, 352, 355, 368, 382, 387, 389, 395, 412, 438, 439, 458, 460, 467, 486, 487, 488, 489, 493, 494, 499, 500, 501, 503, 504, 505, 506, 510, 526, 531, 532, 533, 537, 556, 557, 563, 565, 573, 574, 579, 581, 584, 588, 594]
The total number of sites are: 532

 The number of sites where all mutants are negative for effect: 80

 The percent of sites where all mutants are negative for effect: 15

def make_bubbleplot_entry_region(df):  # Create a bubble plot using Altair for contact site mutants
    barrel_ranges = {
        "Hydrophobic": config["hydrophobic"],
        "Salt Bridges": config["salt_bridges"],
        "Hydrogen Bonds": config["h_bond_total"],
        "Contact": config["contact_sites"],
    }
    custom_order = [
        "Hydrophobic",
        "Salt Bridges",
        "Hydrogen Bonds",
        "Contact",
    ]
    empty_chart = []
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, fields=["site"], value=1
    )
    
    for selection in ["CHO-bEFNB2", "CHO-bEFNB3"]:
        agg_means = []
        tmp_df = df[df["cell_type"] == selection]
        mean_df = tmp_df.groupby("site")[["effect"]].mean().reset_index()

        # For each barrel, filter the site_means dataframe to the sites belonging to that barrel and then store the means
        for barrel, sites in barrel_ranges.items():
            subset = mean_df[mean_df["site"].isin(sites)]
            for _, row in subset.iterrows():
                agg_means.append(
                    {"barrel": barrel, "effect": row["effect"], "site": row["site"]}
                )
        agg_means_df = pd.DataFrame(agg_means)
        chart = (
            alt.Chart(agg_means_df, title=f"{selection}")
            .mark_point(size=200,filled=True)
            .encode(
                x=alt.X(
                    "barrel:O",
                    sort=custom_order,
                    title='Contact Type',
                    axis=alt.Axis(labelAngle=-90),
                ),
                y=alt.Y(
                    "effect",
                    title="Cell Entry",
                    axis=alt.Axis(grid=True, tickCount=4),
                ),
                xOffset="random:Q",
                tooltip=["barrel", "effect", "site"],
                size=alt.condition(
                    variant_selector, alt.value(100), alt.value(50)
                ),
                color=alt.condition(
                    variant_selector, alt.value("orange"), alt.value("black")
                ),
                opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.3)),
            ).properties(height=200,width=200)
            .transform_calculate(random="sqrt(-1*log(random()))*cos(2*PI*random())")
        )
        empty_chart.append(chart)
    combined_effect_chart = (
        alt.hconcat(*empty_chart)
        .resolve_scale(y="shared", x="shared", color="independent")
        .add_params(variant_selector)
    )
    return combined_effect_chart


tmp_img = make_bubbleplot_entry_region(concat_df)
tmp_img.display()
if entry_region_boxplot_plot is not None:
    tmp_img.save(contact_type_plot)

def make_bubbleplot_wildtype_prop(df):
    barrel_ranges = {
        "hydrophobic": list(["A", "V", "L", "I", "M"]),
        "aromatic": list(["Y", "W", "F"]),
        "positive": list(["K", "R", "H"]),
        "negative": list(["E", "D"]),
        "hydrophilic": list(["S", "T", "N", "Q"]),
        "special": list(["C", "P", "G"]),
    }
    empty_charts = []
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, nearest=True, fields=["site"], value=1
    )
    for selection in ["CHO-bEFNB2", "CHO-bEFNB3"]:
        if selection == "CHO-bEFNB2":
            effect_name = "EFNB2"
        else:
            effect_name = "EFNB3"

        tmp_df = df[df["cell_type"] == selection]

        unique_wildtype_df = tmp_df[["site", "wildtype"]].drop_duplicates()
        mean_df = tmp_df.groupby("site")[["effect"]].mean().reset_index()
        mean_df = pd.merge(mean_df, unique_wildtype_df, on="site", how="left")

        agg_means = []

        # For each barrel, filter the site_means dataframe to the sites belonging to that barrel and then store the means
        for barrel, sites in barrel_ranges.items():
            subset = mean_df[mean_df["wildtype"].isin(sites)]
            for _, row in subset.iterrows():
                agg_means.append(
                    {"wildtype_class": barrel, "effect": row["effect"], "site": row["site"], "wildtype": row["wildtype"]}
                )
        agg_means_df = pd.DataFrame(agg_means)

        chart = (
            alt.Chart(agg_means_df, title=f"{selection}")
            .mark_point(size=100,filled=True)
            .encode(
                x=alt.X(
                    "wildtype_class:O",
                    title="Wildtype amino-acid property",
                    axis=alt.Axis(labelAngle=-90),
                ),  
                y=alt.Y(
                    "effect",
                    title=f"Cell Entry",
                    axis=alt.Axis(grid=True, tickCount=4),
                ),
                xOffset="random:Q",
                tooltip=["wildtype_class", "effect", "site","wildtype"],
                size=alt.condition(variant_selector, alt.value(120), alt.value(50)),
                color=alt.condition(
                    variant_selector, alt.value("orange"), alt.value("black")
                ),
                opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.2)),
            ).properties(width=200,height=200)
            .transform_calculate(random="sqrt(-1*log(random()))*cos(2*PI*random())")
            
        )
        empty_charts.append(chart)
    combined_effect_chart = (
        alt.hconcat(*empty_charts)
        .resolve_scale(y="shared", x="shared", color="independent")
        .add_params(variant_selector)
    )
    return combined_effect_chart


wildtype_aa_bubble_img = make_bubbleplot_wildtype_prop(concat_df)
wildtype_aa_bubble_img.display()

# Import distance data
e2_distances = pd.read_csv(e2_distances_file)
distance_df = pd.merge(
    merged_df, e2_distances[["site", "distance"]], on="site", how="left"
)

def determine_distance(df):
    # Define the conditions
    conditions = [
        df["distance"] < 4,
        (df["distance"] >= 4) & (df["distance"] <= 8),
        df["distance"] > 8,
    ]

    # Define the associated values for the conditions
    choices = ["contact", "close", "distant"]

    # Apply the conditions and choices to the 'E2_contact' column
    df["contact"] = np.select(conditions, choices, default="distant")
    return df


distance_df = determine_distance(distance_df)
display(distance_df)

def median_correlation_plot(df, metric):
    aggregation = getattr(df.groupby('site')[["effect_E2", "effect_E3"]], metric)
    means = aggregation().reset_index()
    slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(
        means["effect_E2"], means["effect_E3"]
    )
    display(r_value.round(2))

    means = means.rename(
        columns={"effect_E2": f"{metric}_E2", "effect_E3": f"{metric}_E3"}
    )

    contact_sites = df[["site", "contact", "wildtype"]].drop_duplicates()
    df_mean = pd.merge(means, contact_sites, on="site", how="left")

    chart = (
        alt.Chart(df_mean)
        .mark_point(filled=True,size=60,stroke='black',strokeWidth=1)
        .encode(
            x=alt.X(f"{metric}_E2", title="Entry in CHO-bEFNB2"),
            y=alt.Y(f"{metric}_E3", title="Entry in CHO-bEFNB3"),
            tooltip=["site", "wildtype"],
            color=alt.Color(
                "contact",
                scale=alt.Scale(
                    domain=["contact", "close", "distant"],
                    range=["#1f4e79", "#ff7f0e", "gray"],
                ),
                legend=alt.Legend(title="Receptor distance"),
            ),
        )
    ).properties(width=200,height=200)
    min_ = int(df_mean[f"{metric}_E2"].min())
    max_ = int(df_mean[f"{metric}_E3"].max())
    text = (
        alt.Chart({"values": [{"x": min_, "y": max_, "text": f"r = {r_value:.2f}"}]})
        .mark_text(
            align="left",
            baseline="top",
            dx=-20,  # Adjust this for position
            dy=-20,  # Adjust this for position
        )
        .encode(x=alt.X("x:Q"), y=alt.Y("y:Q"), text="text:N")
    )
    plot = chart + text
    return plot


E2_E3_plot = median_correlation_plot(distance_df, "mean")
E2_E3_plot.display()
if entry_region_boxplot_plot is not None:
    E2_E3_plot.save(E2_E3_entry_corr_plot)

0.82

def correlation_plot(df):
    df = df.dropna()
    slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(
        df["effect_E2"], df["effect_E3"]
    )
    display(r_value.round(2))
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, nearest=True, fields=["contact"], value=1
    )
    chart = (
        alt.Chart(df)
        .mark_point(size=40,opacity=1,filled=True)
        .encode(
            x=alt.X("effect_E2", title="Entry in CHO-bEFNB2"),
            y=alt.Y("effect_E3", title="Entry in CHO-bEFNB3"),
            tooltip=["site", "wildtype", "mutant"],
            color=alt.Color(
                "contact",
                scale=alt.Scale(
                    domain=["contact", "close", "distant"],
                    range=["#1f4e79", "#ff7f0e", "gray"],
                ),
                legend=alt.Legend(title="RBP Distance to Receptor"),
            ),
            opacity=alt.condition(variant_selector,alt.value(1),alt.value(0.2)),
        ).add_params(variant_selector)
    )
    min_ = int(df['effect_E2'].min())
    max_ = int(df['effect_E3'].max())
    
    text = (
        alt.Chart({"values": [{"x": min_, "y": max_, "text": f"r = {r_value:.2f}"}]})
        .mark_text(
            align="left",
            baseline="top",
            dx=-20,  # Adjust this for position
            dy=-20,  # Adjust this for position
        )
        .encode(x=alt.X("x:Q"), y=alt.Y("y:Q"), text="text:N")
    )
    plot = chart + text

    return plot


tmp_img_corr = correlation_plot(distance_df)
tmp_img_corr.display()
if entry_region_boxplot_plot is not None:
    tmp_img_corr.save(E2_E3_entry_all_muts_plot)

if entry_region_boxplot_plot is not None:
    (E2_E3_plot | tmp_img_corr).save(combined_E2_E3_correlation_plots)

0.79

def make_boxplot_entry_region(df):
    barrel_ranges = {
        "Stalk": list(range(70, 147)),
        "Neck": list(range(148, 165)),
        "Linker": list(range(166, 177)),
        "Head": list(range(178, 602)),
    }
    custom_order = ["Stalk", "Neck", "Linker", "Head", "Receptor Contact", "Total"]
    empty_charts = []
    for selection in ["CHO-bEFNB2", "CHO-bEFNB3"]:
        if selection == "CHO-EFNB2":
            effect_name = "EFNB2"
        else:
            effect_name = "EFNB3"

        tmp_df = df[df["cell_type"] == selection]
        agg_means = []
        for barrel, sites in barrel_ranges.items():
            subset = tmp_df[tmp_df["site"].isin(sites)]
            for _, row in subset.iterrows():
                agg_means.append(
                    {"region": barrel, "effect": row["effect"], "site": row["site"]}
                )
            agg_means_df = pd.DataFrame(agg_means)
        chart = (
            alt.Chart(agg_means_df, title=f"{selection}")
            .mark_boxplot(color='darkgray',extent='min-max')
            .encode(
                x=alt.X(
                    "region:O",
                    sort=custom_order,
                    title="RBP Region",
                    axis=alt.Axis(labelAngle=-90),
                ),
                y=alt.Y(
                    "effect",
                    title=f"Cell Entry",
                    axis=alt.Axis(grid=True, tickCount=4),
                ),
                tooltip=["region", "effect", "site"],
            ).properties(width=config['width'],height=config['height'])
        )
        empty_charts.append(chart)
    combined_effect_chart = alt.hconcat(*empty_charts).resolve_scale(
        y="shared", x="shared", color="independent"
    )
    return combined_effect_chart


entry_region_boxplot = make_boxplot_entry_region(concat_df)
entry_region_boxplot.display()
if entry_region_boxplot_plot is not None:
    entry_region_boxplot.save(entry_region_boxplot_plot)

def find_potential_glycan_sites(df):
    filtered = df[df["wildtype"].isin(["T", "S"])]
    matching_sites = []
    for index, row in filtered.iterrows():
        # Check for existence of site two numbers prior with 'N' mutant and positive effect
        prior_rows = df[
            (df["site"] == row["site"] - 2) & (df["mutant"] == "N") & (df["effect"] > 0)
        ]
        if not prior_rows.empty:
            matching_sites.append(row["site"])
    unique_list1 = list(set(matching_sites))
    unique_list1 = [x - 2 for x in unique_list1]

    filtered = df[df["wildtype"].isin(["N"])]
    matching_sites = []
    for index, row in filtered.iterrows():
        # Check for existence of site two numbers prior with 'N' mutant and positive effect
        prior_rows = df[
            (df["site"] == row["site"] + 2)
            & (df["mutant"].isin(["T", "S"]))
            & (df["effect"] > 0)
        ]
        if not prior_rows.empty:
            matching_sites.append(row["site"])
    unique_list2 = list(set(matching_sites))
    unique_list = unique_list1 + unique_list2
    unique_list.sort()
    return unique_list
#call function
PNLG = find_potential_glycan_sites(func_scores_E3)
#read in surface exposure data to find potential glycans on surface of protein
surface_df = pd.read_csv(surface)
surface_df.rename(columns={"exposure_A": "Surface Exposure"}, inplace=True)
PNLG_SURFACE = surface_df[surface_df["site"].isin(PNLG)]
PNLG_SURFACE = list(
    PNLG_SURFACE[PNLG_SURFACE["Surface Exposure"] >= 25]["site"].unique()
)

#print(f"\nThe surface exposed PNLG sites are: {PNLG_SURFACE}\n")

glycans = config["glycans"] #these are the glycan sites that are already present in protein

#filter out known glycan sites already present
filtered_PNLG_SURFACE = [num for num in PNLG_SURFACE if num not in glycans]
print(f'These are {len(filtered_PNLG_SURFACE)} potential glycan sites one amino acid away: {filtered_PNLG_SURFACE}')
#print(len(filtered_PNLG_SURFACE))

These are 15 potential glycan sites one amino acid away: [180, 191, 192, 311, 326, 359, 383, 403, 423, 473, 478, 543, 554, 570, 600]

def entry_by_site(df):
    tmp_df = df.groupby('site')['effect'].mean().reset_index()
    
    # define ranges of different RBP regions
    barrel_ranges = {
        "Stalk": list(range(70, 148)),
        "Neck": list(range(148, 166)),
        "Linker": list(range(166, 178)),
        "Head": list(range(178, 602)),
    }
    
    custom_order = ["Stalk", "Neck", "Linker", "Head"] #custom order for color legend
    
    agg_means = [] #store aggregation 
    
    # For each barrel, filter the dataframe to the sites belonging to that barrel and then store the means
    for barrel, sites in barrel_ranges.items():
        subset = tmp_df[tmp_df["site"].isin(sites)]
        for _, row in subset.iterrows():
            agg_means.append(
                {"region": barrel, "effect": row["effect"], "site": row["site"]}
            )
        agg_means_df = pd.DataFrame(agg_means).round(3)
    #display(agg_means_df)
    agg_means_df['beta_sheet'] = agg_means_df['site'].isin(config['beta_sheet']) #add a column specifying which sites are in beta sheets
    
    ### The main chart plotting
    chart = (
        alt.Chart(agg_means_df)
        .mark_bar(opacity=1)
        .encode(
            x=alt.X("site:N", title='Site',axis=alt.Axis(labelAngle=-90,values=[100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600],tickCount=11,grid=True)),
            y=alt.Y("effect", title="Mean entry in CHO-bEFNB3"),
            tooltip=["site", "effect","region"],
            color=alt.Color('region',sort=custom_order,title='Region'),
        )
    ).properties(width=1000,height=200)
    
    ### Draw rectanges showing where beta sheets are in protein above chart
    rect = alt.Chart(agg_means_df.query('beta_sheet == True')).mark_rect(color='black').encode(
        alt.X('site:N',axis=None),
        alt.Y('beta_sheet',axis=None)
    ).properties(width=800,height=10)
    
    combined_chart = alt.vconcat(chart,padding=0).resolve_scale(y='independent',x='shared')
    

    return combined_chart

entry_by_site_plot = entry_by_site(func_scores_E3)
entry_by_site_plot.display()

def entry_by_site_region(df,site_list,name_of_title):
    #calculate mean by site
    tmp_df = df.groupby(['site','cell_type'])['effect'].mean().reset_index().round(3) 
    
    #make a unique values df to merge
    unique_wildtypes_df = df.drop_duplicates(subset=['site','wildtype','wt_type','wildtype_site'])
    
    #merge mean and unique values
    tmp_df = pd.merge(tmp_df, unique_wildtypes_df[['site', 'wt_type','wildtype','wildtype_site']], on='site', how='left')

    #filter by site
    tmp_df = tmp_df[tmp_df['site'].isin(site_list)]

    #make chart
    chart = (
        alt.Chart(tmp_df,title=name_of_title)
        .mark_bar(opacity=1)
        .encode(
            x=alt.X("site:N", sort='-y',title='Site',axis=alt.Axis(labelAngle=-90)),
            y=alt.Y("effect", title="Mean entry"),
            tooltip=["site", "effect", 'wildtype', 'wt_type'],
            color=alt.Color('wt_type:N', scale=alt.Scale(scheme='tableau10'), legend=alt.Legend(title="Unmutated amino-acid type"))
        )
    ).properties(width=alt.Step(12), height=100)
    
    return chart

entry_by_site_receptor_plot = entry_by_site_region(func_scores_E3,config['contact_sites'],'Contact Sites')
entry_by_site_receptor_plot.display()

entry_by_site_receptor_plot_stalk = entry_by_site_region(func_scores_E3,list(range(70, 148)),'Stalk')
entry_by_site_receptor_plot_stalk.display()

entry_by_site_receptor_plot_neck = entry_by_site_region(func_scores_E3,list(range(147,175)),'Neck')
entry_by_site_receptor_plot_neck.display()

entry_by_site_receptor_plot_linker = entry_by_site_region(func_scores_E3,list(range(166, 178)),'Linker')
entry_by_site_receptor_plot_linker.display()

combined_region_barplot = alt.vconcat(entry_by_site_receptor_plot_stalk,entry_by_site_receptor_plot_neck,entry_by_site_receptor_plot_linker,entry_by_site_receptor_plot,padding=0).resolve_scale(y="shared", x="independent", color="shared")
combined_region_barplot.display()
combined_region_barplot.save(combined_region_barplot_output)

	site	wildtype	mutant	effect_E2	effect_std_E2	times_seen_E2	n_selections_E2	cell_type_E2	wildtype_site_E2	wt_type_E2	...	effect_E3	effect_std_E3	times_seen_E3	n_selections_E3	cell_type_E3	wildtype_site_E3	wt_type_E3	mutant_type_E3	distance	contact
0	71	Q	C	-1.750	0.1777	4.625	8.0	CHO-bEFNB2	Q71	hydrophilic	...	-0.72270	0.7828	3.000	7.0	CHO-bEFNB3	Q71	hydrophilic	special	NaN	distant
1	71	Q	D	-1.164	0.8890	4.500	8.0	CHO-bEFNB2	Q71	hydrophilic	...	-0.38840	0.6369	3.429	7.0	CHO-bEFNB3	Q71	hydrophilic	negative	NaN	distant
2	71	Q	E	-1.255	0.3123	5.375	8.0	CHO-bEFNB2	Q71	hydrophilic	...	-0.24820	0.9791	4.571	7.0	CHO-bEFNB3	Q71	hydrophilic	negative	NaN	distant
3	71	Q	F	-1.058	0.6637	4.625	8.0	CHO-bEFNB2	Q71	hydrophilic	...	-0.49730	0.3080	3.286	7.0	CHO-bEFNB3	Q71	hydrophilic	aromatic	NaN	distant
4	71	Q	G	-1.425	0.5878	7.875	8.0	CHO-bEFNB2	Q71	hydrophilic	...	-1.33100	0.8316	4.714	7.0	CHO-bEFNB3	Q71	hydrophilic	special	NaN	distant
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
9934	595	V	T	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	-0.32370	0.5694	2.143	7.0	CHO-bEFNB3	V595	hydrophobic	hydrophilic	17.838812	distant
9935	599	E	A	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	0.17320	0.4067	3.143	7.0	CHO-bEFNB3	E599	negative	hydrophobic	30.234262	distant
9936	600	Q	V	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	0.31020	0.1140	3.571	7.0	CHO-bEFNB3	Q600	hydrophilic	hydrophobic	30.670734	distant
9937	601	C	I	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	-0.75770	0.9218	2.286	7.0	CHO-bEFNB3	C601	special	hydrophobic	29.834501	distant
9938	601	C	V	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	0.01403	0.7747	3.000	4.0	CHO-bEFNB3	C601	special	hydrophobic	29.834501	distant

nipah_RBP_entry_analysis.ipynb¶

This notebook pulls in data on Nipah RBP entry into CHO-bEFNB2 and bCHO-EFNB3 cells, calculates stats, and makes figures¶

Paths for running notebook interactively¶

Read in custom altair theme and import YAML file with parameters¶

Import filtered data¶

Calculate some basic stats about E2 and E3 entry scores¶

Find which sites only have negative entry scores for all mutants¶

Make bubble plots of receptor contact site type (median values per site)¶

Make bubble plots depending on amino acid property¶

Plot correlations between E2 and E3 entry¶

Make boxplot showing median entry by RBP region¶

Check for potential neutral/beneficial glycosylation sites¶

Make bar plot of average entry scores for CHO-bEFNB3¶

Make bar charts of mean cell entry by site for different regions, sorted by average and colored by the unmutated amino acid at position¶

Ranked average entry in contact sites¶

Now make ranked averages for each region¶

Ranked average entry in RBP stalk¶

Ranked average entry in RBP neck¶

Ranked average entry in RBP linker¶